NEW YORK — When the Obama administration announced an expanded immigration initiative this week to address an escalating humanitarian crisis in Central America, it seemed almost paradoxical.

On one hand, the government was broadening a program for children fleeing three violence-racked countries there, allowing for more applicants to come to the United States as refugees.

At the same time, the federal government continued to deport young people from Central America who crossed the border and asked for protection — sending some of them back to those same countries.

“Government is a big and complicated beast, and it can do contradictory things at the same time,” said Eve Stotland, the legal director of The Door, an organization that works with young people in New York. One of the group’s clients, a teenager from Guatemala, was almost deported this month.

“It is possible for one part of government to be taking action to protect certain Central American children, and at the same time take other actions which endanger Central American children,” Stotland added.

In 2014, President Barack Obama declared a crisis at the U.S.-Mexico border in response to a wave of tens of thousands of people, many of them unaccompanied children, fleeing the extreme gang violence gripping El Salvador, Honduras and Guatemala. The numbers dipped in 2015, but are surging again this year.

Many of the minors were allowed to enter the United States provided they appeared in immigration court and applied for either asylum or a special status that showed they were abandoned, neglected or abused. About 10 percent of those minors settled in New York state.

The government first created a program for Central American minors in December 2014; it admitted children with parents living legally in the United States. With the latest plan, minors, along with family members, will be processed in Costa Rica.

“I think the desire is to create a process of orderly entry rather than disorderly exit,” said Mario Russell, the director of immigrant and refugee services for Catholic Charities Community Services of New York, an agency designated to administer the program. “It’s probably to send the message that ‘we’re going to try to shut down the pipeline, but we’re not going to eliminate the options,'” he added. “Even if it’s a fraction of what’s really necessary.”

But the pace has been glacial, according to Russell. Of the 150 applications his organization filed, only three children have arrived with refugee status. Only six have qualified to come under parole, designated case by case for urgent humanitarian reasons. About half of the cases are still pending, Russell said.

Toward the end of 2014, the Department of Homeland Security tightened the United States’ southern border and sent warnings to migrants trying to make the dangerous crossing.

Since the beginning of this year, when Immigration and Customs Enforcement carried out raids on children and families who had orders of removal, the government has continued to enforce its priorities: recent border crossers who had exhausted all legal avenues, such as being denied asylum, and those who were ordered deported.

This year, the New York field office of the customs agency has detained for deportation seven young adults since they have turned 18 after crossing the border.

“Not only have enforcement priorities not changed, but ICE’s position has remained inflexible despite clients having eligibility for relief,” said Gui Stampur, the director of Safe Passage Project at New York Law School, which represents unaccompanied minors in immigration court.

Jeh C. Johnson, the Homeland Security secretary, has said that “immigration policy must be two sides of the same coin.” In a statement this month in which he released the latest numbers for immigrants apprehended at the Mexican border, he noted that “we must enforce our immigration laws” but also acknowledge that conditions in Central America “push many to flee the region in search of a better life in the United States.”

“We recognize the need to provide a safe alternative path to our country and that many from the region should be regarded as refugees,” he continued.

Russell said that once they are here, young migrants without access to lawyers struggle to navigate the immigration courts; 9 in 10 minors who appeared without lawyers were ordered deported, according to a report by the Transactional Records Access Clearinghouse, a group that studies federal data.

Because the minors program is limited to children who have a parent in the United States with legal status, many young adults like the Door’s client, Brayan, 19, never would have been eligible.

Brayan, who spoke in Spanish through an interpreter, discussed his situation on the condition that only his first name be used because of his continuing legal case.

He crossed the border on his own in 2015, when he was 17, to flee gang violence in Guatemala and came to live with a cousin in Queens. In June of that year, he appeared in immigration court, without a lawyer. Shortly after, his cousin returned to Guatemala, leaving Brayan to scramble to find a place to live. He missed his next scheduled court date in August and was issued a removal order in absentia, as is the judge’s right.

Brayan said he did not get the order because he had moved in with a friend. Then in May of this year, just before his 19th birthday, he said, he was woken up by a series of calls on his cellphone from a blocked number. On the 12th call, he answered. The caller said he was a federal official.

“When I heard federal, I thought, ‘Well, I don’t have a problem with federal because that’s criminal,'” Brayan said. “The federals are looking for criminals.”

He met with the caller and was detained, then taken to the Hudson County Jail in New Jersey. Another cousin found a flier for the Door in Brayan’s jacket pocket, and he called the organization.

A year earlier, one of the group’s lawyers had screened Brayan at his first court appearance, as part of a city and privately funded program known as ICare.

Brayan’s lawyer, Amy Pont, argued that exceptional circumstances existed for why he missed his hearing and that he should not be deported. In mid-July, the government agreed to reopen his case and schedule a February hearing. He was released from the detention center.

Asked whether he would warn his friends who wanted to flee the gang violence how difficult it would be, Brayan said he was worried how they would perceive such advice.

“It’s like if I tell them, ‘Don’t come because it’s hard, there is a lot of immigration and it’s a difficult journey,’ they’ll say, ‘Well, then you’re selfish,'” he said.